GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PG_binding_1 - Putative peptidoglycan binding domain
Pfam: PF01471 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0244
Length: 57
Sequences: 6160
Seq/Len: 108.07
HH_delta: -0.131 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
31_R35_K1.941572.722
46_T50_D1.529292.144
17_Y40_A1.508532.115
8_L49_V1.420991.992
38_Q47_G1.249871.752
37_F41_N1.243111.743
9_Q24_G1.239821.738
50_D53_T1.231491.726
37_F56_A1.150571.613
35_K45_V1.136071.593
26_F34_V1.129581.584
9_Q27_D1.117171.566
39_K45_V1.116881.566
49_V54_W1.091491.530
26_F31_R1.059371.485
38_Q53_T1.034221.450
5_V26_F1.02431.436
41_N56_A0.987151.384
23_D27_D0.984571.380
9_Q30_T0.950281.332
51_P55_E0.894411.254
38_Q46_T0.85181.194
13_N22_V0.829561.163
8_L34_V0.818321.147
11_Y15_L0.771331.081
3_P6_K0.741881.040
43_L53_T0.720751.010
11_Y14_R0.719641.009
4_D7_A0.699430.981
11_Y57_L0.690220.968
27_D30_T0.682870.957
6_K10_Q0.681580.956
13_N19_P0.678040.951
10_Q14_R0.663570.930
13_N18_Y0.66180.928
36_A40_A0.647970.908
34_V49_V0.646440.906
7_A11_Y0.628310.881
52_E55_E0.625770.877
15_L41_N0.617950.866
28_P32_E0.616230.864
6_K24_G0.607410.852
34_V53_T0.605620.849
7_A10_Q0.574620.806
15_L57_L0.570410.800
8_L57_L0.558170.783
4_D54_W0.546820.767
18_Y33_A0.544820.764
32_E36_A0.543030.761
35_K39_K0.542870.761
29_E32_E0.535410.751
6_K22_V0.533870.748
9_Q23_D0.524430.735
20_G29_E0.518470.727
35_K47_G0.514670.722
13_N20_G0.511480.717
17_Y20_G0.507910.712
17_Y36_A0.501660.703
32_E35_K0.493990.693
15_L40_A0.492640.691
16_G33_A0.48570.681
5_V30_T0.479270.672
52_E56_A0.471350.661
18_Y29_E0.470360.659
10_Q22_V0.468670.657
23_D29_E0.467360.655
21_P29_E0.465830.653
49_V53_T0.449090.630
37_F53_T0.446190.626
38_Q50_D0.43890.615
19_P29_E0.438320.614
44_P52_E0.433160.607
18_Y22_V0.428790.601
13_N21_P0.423340.593
36_A39_K0.414630.581
25_I28_P0.413060.579
7_A54_W0.410040.575
9_Q22_V0.400810.562
31_R48_V0.398290.558
26_F30_T0.394770.553
7_A14_R0.383630.538
33_A36_A0.381240.534
28_P31_R0.379220.532
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
4fetB199.1-0.131
3bkhA199.1-0.123
1lbuA198.9-0.072
4g54A198.9-0.051
3d2yA0.964998.70.019
1l6jA198.40.126
1eakA0.947498.20.175
1ck7A0.947498.20.176
1su3A198.20.19
1slmA198.10.196

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